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- PDB-3ap5: Crystal structure of the galectin-8 N-terminal carbohydrate recog... -

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Basic information

Entry
Database: PDB / ID: 3ap5
TitleCrystal structure of the galectin-8 N-terminal carbohydrate recognition domain
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / Beta-Sandwich / Galectin / Carbohydrate/Sugar Binding
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsMatsuzaka, T. / Ideo, H. / Yamashita, K. / Nonaka, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Galectin-8-N-domain recognition mechanism for sialylated and sulfated glycans
Authors: Ideo, H. / Matsuzaka, T. / Nonaka, T. / Seko, A. / Yamashita, K.
History
DepositionOct 11, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-8


Theoretical massNumber of molelcules
Total (without water)17,4231
Polymers17,4231
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.055, 76.055, 66.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17423.123 Da / Num. of mol.: 1 / Fragment: N-terminal carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS CAUSED BY NATURAL VARIANT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.275mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.28 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2005
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.92→34.021 Å / Num. all: 15467 / Num. obs: 15467 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 25.591 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1112 / Rsym value: 0.239 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APB

3apb


Resolution: 1.92→34.01 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.499 / SU ML: 0.103 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23651 775 5 %RANDOM
Rwork0.20408 ---
obs0.20569 14649 99.92 %-
all-14649 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 116 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221247
X-RAY DIFFRACTIONr_bond_other_d0.0010.02868
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9511689
X-RAY DIFFRACTIONr_angle_other_deg0.74732112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30323.55959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69615215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4781.5757
X-RAY DIFFRACTIONr_mcbond_other0.0841.5306
X-RAY DIFFRACTIONr_mcangle_it0.91721238
X-RAY DIFFRACTIONr_scbond_it1.3423490
X-RAY DIFFRACTIONr_scangle_it2.2714.5451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 53 -
Rwork0.241 1051 -
obs--99.91 %

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